FMO DATABASE

FMODB ID: V21Y1

Calculation Name: 1K46-A-Xray309

Preferred Name: Tyrosine-protein phosphatase yopH

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1K46

Chain ID: A

ChEMBL ID: CHEMBL5835

UniProt ID: P08538

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-924629.828007
FMO2-HF: Nuclear repulsion	877336.666082
FMO2-HF: Total energy	-47293.161926
FMO2-MP2: Total energy	-47432.195711

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:ACE )

Summations of interaction energy for fragment #1(A:1:ACE )

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-0.24	0.821	0.18	-0.347	-0.893	0

Interaction energy analysis for fragmet #1(A:1:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.004

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	LEU	0	0.026	-0.006	3.847	1.179	1.883	-0.006	-0.341	-0.357	0.001
4	A	4	SER	0	0.063	0.034	7.227	-0.118	-0.118	0.000	0.000	0.000	0.000
5	A	5	LEU	0	0.059	0.024	10.689	-0.048	-0.048	0.000	0.000	0.000	0.000
6	A	6	SER	0	-0.013	-0.005	12.054	0.025	0.025	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.828	-0.920	11.566	-0.249	-0.249	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.007	0.018	7.630	0.024	0.024	0.000	0.000	0.000	0.000
9	A	9	HIS	0	0.035	0.011	10.627	0.056	0.056	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.939	0.980	14.049	0.293	0.293	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.086	-0.059	9.687	0.011	0.011	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.038	0.013	11.541	0.041	0.041	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.002	-0.004	14.075	0.051	0.051	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.918	0.965	15.546	0.196	0.196	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.000	0.000	13.110	0.022	0.022	0.000	0.000	0.000	0.000
16	A	16	VAL	0	0.027	0.017	17.435	0.021	0.021	0.000	0.000	0.000	0.000
17	A	17	GLN	0	-0.062	-0.040	19.645	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.071	-0.032	18.882	0.013	0.013	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.921	-0.952	22.122	-0.060	-0.060	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.026	-0.018	18.420	0.013	0.013	0.000	0.000	0.000	0.000
21	A	21	GLY	0	-0.032	-0.028	18.512	-0.017	-0.017	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.905	-0.935	19.010	-0.126	-0.126	0.000	0.000	0.000	0.000
23	A	23	CYS	0	-0.104	-0.033	17.424	0.012	0.012	0.000	0.000	0.000	0.000
24	A	24	THR	0	0.013	0.012	13.737	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.021	0.012	11.350	0.018	0.018	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.934	0.953	9.141	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.007	0.014	2.995	-0.118	-0.081	0.178	0.083	-0.298	-0.001
28	A	28	ARG	1	0.958	0.980	4.661	-0.719	-0.612	0.000	-0.012	-0.095	0.000
29	A	29	GLY	0	0.036	0.017	4.531	-0.374	-0.386	0.000	-0.010	0.022	0.000
30	A	30	ASN	0	-0.036	-0.029	5.221	0.238	0.313	0.000	-0.002	-0.072	0.000
31	A	31	VAL	0	0.014	0.021	7.388	-0.093	-0.093	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.016	0.012	9.357	-0.073	-0.073	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.020	-0.016	12.848	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	34	ASN	0	0.029	0.004	15.538	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.914	0.946	17.413	-0.164	-0.164	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.926	-0.943	20.383	0.033	0.033	0.000	0.000	0.000	0.000
37	A	37	THR	0	0.009	0.015	20.265	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	38	THR	0	0.004	-0.008	20.996	0.010	0.010	0.000	0.000	0.000	0.000
39	A	39	PHE	0	-0.036	-0.023	18.856	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	40	GLN	0	-0.035	-0.028	21.025	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.029	0.023	20.671	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.057	-0.017	20.242	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	43	THR	0	0.049	0.011	18.832	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.018	-0.015	15.337	0.008	0.008	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.038	-0.019	19.256	0.009	0.009	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.020	-0.002	22.299	0.004	0.004	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.052	0.020	22.259	0.010	0.010	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.037	0.004	16.941	0.010	0.010	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.906	0.928	15.589	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.840	-0.942	13.290	-0.236	-0.236	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.044	-0.028	10.594	-0.049	-0.049	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.803	-0.871	10.343	0.087	0.087	0.000	0.000	0.000	0.000
53	A	53	LYS	1	1.015	1.016	11.743	0.248	0.248	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.033	-0.001	6.187	-0.045	-0.045	0.000	0.000	0.000	0.000
55	A	55	PHE	0	-0.037	0.007	7.230	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.045	0.013	8.160	0.026	0.026	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.055	0.007	9.357	-0.024	-0.024	0.000	0.000	0.000	0.000
58	A	58	THR	0	0.001	0.006	3.530	-0.397	-0.284	0.008	-0.051	-0.070	0.000
59	A	59	VAL	0	-0.019	-0.009	6.227	0.103	0.103	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.015	-0.008	8.676	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.033	-0.024	7.428	-0.033	-0.033	0.000	0.000	0.000	0.000
62	A	62	HIS	0	-0.066	-0.034	4.041	0.030	0.067	0.000	-0.014	-0.023	0.000
63	A	63	VAL	0	-0.013	-0.007	9.240	0.033	0.033	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.032	0.031	12.332	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.085	-0.060	14.269	0.011	0.011	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.037	0.014	14.108	0.011	0.011	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.033	-0.018	17.172	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.036	-0.011	17.318	0.016	0.016	0.000	0.000	0.000	0.000
69	A	69	THR	0	0.016	-0.001	21.102	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	70	GLN	0	0.069	0.041	24.188	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.857	-0.951	25.095	0.054	0.054	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.799	-0.852	20.469	0.099	0.099	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.003	-0.012	22.428	0.000	0.000	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.003	0.007	23.780	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.931	0.962	22.191	-0.112	-0.112	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.028	0.019	18.135	0.001	0.001	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.022	0.024	22.134	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	78	GLN	0	0.004	0.003	25.653	0.000	0.000	0.000	0.000	0.000	0.000
79	A	79	SER	0	-0.021	-0.001	20.804	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.032	-0.021	23.648	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.015	-0.011	25.045	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.900	0.951	24.704	-0.082	-0.082	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.071	-0.045	21.994	0.004	0.004	0.000	0.000	0.000	0.000
84	A	84	ASN	0	-0.042	-0.010	26.222	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.039	0.021	22.475	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	86	ASN	0	0.008	-0.002	23.866	0.011	0.011	0.000	0.000	0.000	0.000
87	A	87	ASN	0	0.012	0.015	16.786	-0.021	-0.021	0.000	0.000	0.000	0.000
88	A	88	TYR	0	-0.021	-0.058	16.117	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.797	-0.845	19.815	-0.046	-0.046	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.017	-0.005	20.156	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.947	0.974	21.741	0.042	0.042	0.000	0.000	0.000	0.000
92	A	92	SER	0	0.026	-0.003	24.508	0.004	0.004	0.000	0.000	0.000	0.000
93	A	93	VAL	0	-0.061	-0.027	23.984	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.017	0.002	26.922	0.000	0.000	0.000	0.000	0.000	0.000
95	A	95	ASN	0	-0.026	-0.013	29.038	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.046	0.027	29.496	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	97	ASN	0	-0.007	-0.008	24.928	0.010	0.010	0.000	0.000	0.000	0.000
98	A	98	SER	0	-0.007	-0.005	23.047	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	99	VAL	0	0.021	0.019	18.910	0.005	0.005	0.000	0.000	0.000	0.000
100	A	100	LEU	0	0.001	0.011	14.709	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	101	VAL	0	-0.051	-0.033	17.213	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	102	SER	0	-0.029	-0.040	16.475	-0.025	-0.025	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.018	-0.008	13.064	0.022	0.022	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.811	0.910	17.393	0.018	0.018	0.000	0.000	0.000	0.000
105	A	105	SER	0	-0.019	-0.025	18.160	0.006	0.006	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.862	-0.936	15.061	-0.140	-0.140	0.000	0.000	0.000	0.000
107	A	107	GLN	0	0.004	-0.011	14.700	0.006	0.006	0.000	0.000	0.000	0.000
108	A	108	MET	0	0.031	0.012	12.715	0.009	0.009	0.000	0.000	0.000	0.000
109	A	109	THR	0	-0.010	0.015	14.407	0.038	0.038	0.000	0.000	0.000	0.000
110	A	110	LEU	0	0.052	0.000	12.540	0.010	0.010	0.000	0.000	0.000	0.000
111	A	111	GLN	0	-0.029	-0.011	14.948	0.026	0.026	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.733	-0.844	16.579	0.099	0.099	0.000	0.000	0.000	0.000
113	A	113	ALA	0	0.006	-0.001	11.264	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.853	0.942	13.007	-0.191	-0.191	0.000	0.000	0.000	0.000
115	A	115	VAL	0	0.004	-0.002	14.863	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	116	LEU	0	0.009	-0.001	13.738	-0.007	-0.007	0.000	0.000	0.000	0.000
117	A	117	LEU	0	0.011	-0.006	8.686	0.003	0.003	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.897	-0.945	12.551	0.221	0.221	0.000	0.000	0.000	0.000
119	A	119	ALA	0	-0.022	0.004	15.822	-0.020	-0.020	0.000	0.000	0.000	0.000
120	A	120	ALA	0	0.007	-0.012	12.520	-0.020	-0.020	0.000	0.000	0.000	0.000
121	A	121	LEU	0	0.014	0.015	12.583	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	122	ARG	1	0.782	0.865	15.319	-0.127	-0.127	0.000	0.000	0.000	0.000
123	A	123	GLN	0	0.004	0.003	17.314	-0.013	-0.013	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.979	-0.981	13.111	0.222	0.222	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.079	-0.029	17.060	-0.015	-0.015	0.000	0.000	0.000	0.000
126	A	126	NME	0	-0.025	-0.015	19.802	-0.015	-0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:ACE )